I don't think it matters what system the characters came from (except for the Ice Climbers, who were explicitly included to be arcade-style NES representatives). The fact is, most of Nintendo's franchises were established on the NES, or at least really early on... notice, in All-Star mode, the jump between Pokémon, from the later years of the Game Boy, to Pikmin, from just before Melee.
Of course, there are some complications--Ike isn't that old, but he's way back there because of the oldness of Fire Emblem and Marth. Ness and Lucas appear earlier than they would if not for MOTHER, even though Ninten is absent.